1. Field of the Invention
The invention relates generally to novel and substantially improved compositions and methods for providing DNA fragments derived from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies etc.), and for analyses of same.
2. Background Information
Samples or biopsies are archived many times by default in diagnostic routines. This is done in order to conserve the tissue and to prepare it for subsequent histological examinations. Such conservation is necessary to ensure that the biopsy has not changed after the removal, the observed findings correspond to the situation of the patient, and to prevent degradation of cell structures. Accordingly, the tissue sample is immediately put into a fixative for example formalin after removal. After fixation, the sample is embedded into paraffin, which allows a sectioning of the tissue and a subsequent further histological examination.
Using these procedures, biopsies are routinely taken from patients for diagnosing diseases and/or for studying the pattern of markers associated with diseases. Over the last decades, millions of biopsies were collected, archived and stored in this way. These samples represent a major resource for the detection or analysis of disorders or disease associated alterations. Therefore, these samples are invaluable because they allow the evaluation of diagnostic and/or prognostic indicators in retrospective collections.
But unfortunately, this resource is only minimally accessible by molecular biological means, in particular by the most promising and modern methods such as those for the analysis of the methylation pattern. This is because of difficulties in obtaining sufficiently large amounts of high quality genomic DNA at low costs and with minimal handling effort.
These difficulties are based on the degradation of DNA and RNA due to fixation and storage conditions of the sample or biopsy, and on the insufficient methods for the preparation of DNA. To preserve morphological structures in the sample as well as possible, biopsies are usually fixed very well. This has the disadvantage that a lot of proteins are covalently linked to the genomic DNA and also the genomic DNA becomes cross-linked. Consequently, genomic DNA tends to be of small fragment size, has a low integrity, and is contaminated by proteins, peptides and/or amino acids which are cross linked with the DNA and which also interfere with further analysis.
Most prior art methods for the isolation of DNA from paraffin embedded formalin-fixed tissues are based on methods for the isolation of DNA from fresh tissue. They are carried out as one skilled in the art would treat fresh samples maybe with an additional paraffin removal step. As it is well known, such a procedure leads only to comparably low yields of genomic DNA, the DNA having only a small fragment length. Furthermore, the DNA is also not suitable for more sophisticated analysis methods, because still a lot of interfering proteins, peptides and/or amino acids are linked to the DNA.
Particular ‘improved’ methods are known in the art. For example U.S. Pat. No. 6,248,535 teaches a method for the isolation of nucleic acids from paraffin embedded formalin-fixed tissue. According to this method, the sample gets deparaffinized, homogenized before it is heated in a chaotropic solution. After mixing with chloroform, following centrifugation, the solution has three phases. The interphase contains the genomic DNA.
A different method is described by GB 2369822. According to this, sections of a paraffin-embedded formalin-fixed sample are put into a tube. A detergent, a wax and a tissue-digesting enzyme are added, before the tube is heated to about 60° C. for about 30 min. After this the enzyme is inactivated by a temperature increase to 96° C. A subsequent centrifugation step leads to a layering inside the tube, the middle layer containing the genomic DNA as well the RNA.
Such methods usually lead to larger amounts of genomic DNA with a lot of contaminating RNA and protein. In addition, the contaminants cannot be easily removed because they are cross-linked to the genomic DNA by the fixative. Moreover, in principle, it may be possible to also isolate longer nucleic acid fragments with these kinds of methods, but the portion of long fragments is very small.
Several proposals have been made to get longer fragments: Bonin et al. teach a filling in of single-stranded breaks after isolation of the DNA and a denaturing step before PCR amplification (Bonin S., Petrera, F., Niccolini, B., Stanta, G. (2003) J. Clin. Pathol: Mol. Pathol. 56, 184-186). According to this method fragments up to 300 bp are amplifiable.
Inadome et al. suggest the isolation of the portion of longer DNA fragments by HPLC (Inadome, Y., Noguchi, M. (2003) Diagn. Mol. Pathol. 12, 231-236). This procedure leads only to very low yields of DNA.
To enlarge the amount of long DNA fragments isolated from paraffin-embedded, formalin-fixed tissues, a whole genome amplification was suggested by Tie et al. and Siwoski et al. (Tie, J., Serizawa, Y., Oshida, S., Usami, R., Yoshida Y. (2005) Pathol. Int. 55, 343-347; Siwoski, A., Ishkanian, A., Garnis, C., Zhang, L., Rosin, M., Lam, W. L. (2002) Mod. Pathol. 15, 889-892.. This solution has the disadvantage of a low reproducibility and is not applicable when DNA is going to be analyzed for methylation as amplification erases methylation signals.
Consequently, genomic DNA isolated according to prior art methods is not suitable for analysis of the methylation pattern as explained in detail below.
The importance of DNA methylation pattern analyses has been revealed in recent years. Many diseases, in particular cancer diseases, are accompanied by modified gene expression. This may be a mutation of the genes themselves, which leads to an expression of modified proteins or to an inhibition or over-expression of the proteins or enzymes. A modulation of the expression may however also occur by epigenetic modifications, in particular by changes in the DNA methylation pattern. Such epigenetic modifications do not affect the actual DNA coding sequence. It has been found that DNA methylation processes have substantial implications for health, and it seems to be clear that knowledge about methylation processes and modifications of the methyl metabolism and DNA methylation are essential for understanding diseases, for the prophylaxis, diagnosis and therapy of diseases.
The precise control of genes, which represents a small part only of the complete genome of mammals, involves regulation in consideration of the fact that the main part of the DNA in the genome is not coding. The presence of such ‘trunk’ DNA containing introns, repetitive elements and potentially actively transposable elements, requires effective mechanisms for their durable suppression (silencing). Apparently, the methylation of cytosine by S-adenosylmethionine (SAM) dependent DNA methyl transferases, which form 5-methylcytosine, represents such a mechanism for the modification of DNA-protein interactions. Genes can be transcribed by methylation-free promoters, even when adjacent transcribed or not-transcribed regions are widely methylated. This permits the use and regulation of promoters of functional genes, whereas the trunk DNA including the transposable elements is suppressed. Methylation also takes place for the long-term suppression of X-linked genes and may lead to either a reduction or an increase of the degree of transcription, depending on where the methylation in the transcription units occurs.
Nearly the complete natural DNA methylation in mammals is restricted to cytosine-guanosine (CpG) dinucleotide palindrome sequences, which are controlled by DNA methyl transferases. CpG dinucleotides are about 1 to 2% of all dinucleotides and are concentrated in CpG islands. According to an art-recognized definition, a region is considered as a CpG island when the C+G content over 200 bp is at least 50% and the percentage of the observed CG dinucleotides in comparison to the expected CG dinucleotides is larger than 0.6 (Gardiner-Garden, M., Frommer, M. (1987) J. Mol. Biol. 196, 261-282). Typically, CpG islands have at least 4 CpG dinucleotides in a sequence of a length of 100 bp.
CpG islands located in promotor regions frequently have a regulatory function for the expression of the corresponding gene. For example, in case the CpG island is hypomethylated, the gene can be expressed. On the other hand, hypermethylation frequently leads to a suppression of the expression. Normally tumor suppressor genes are hypomethylated, but if they become hypermethylated, their expression becomes suppressed. This is observed many times in tumor tissues. By contrast, oncogenes are hypermethylated in healthy tissue, whereas they are hypomethylated in many times in tumor tissues.
The methylation of cytosine has the effect that the binding of proteins is normally prohibited which regulate the transcription of genes. This leads to an alteration of the expression of the gene. Relating to cancer, the expression of genes regulating cell division are thereby altered, for example, the expression of an apoptotic gene is down regulated, while the expression of an oncogene is up regulated. Additionally, hypermethylation may have a long-term influence on regulation. Proteins which deacetylate histones are able to bind via their 5-methyIcytosine binding domain to the DNA when the cytosines get methylated. This results in a deacetylation of the histones, which itself leads to a tighter package of the DNA. Because of that, regulatory proteins are not precluded from binding to the DNA.
Pronounced Need in the Art
The efficient detection of DNA methylation patterns consequently is an important tool for developing new approaches to understand diseases, for the prevention, diagnosis and treatment of diseases and for the screening for disease associated targets. But on the other hand, methods for an efficient detection of DNA methylation require high quality standards in regard to the starting material the genomic DNA. Preferably, the standards are: i) DNA fragment range is between 150 to 1200 bp; and ii) the DNA is free of associated or cross-linked proteins, peptides, amino acids, RNA as well as of nucleotides or bases, which are not part of the DNA backbone.
Furthermore, there are also requirements with regard to the methods according to which the DNA is isolated. The reason for these is that a lot of samples are typically analyzed for developing new approaches for the prevention, diagnosis and treatment of a disease and for the screening for disease associated targets. Preferably, the requirements are: i) isolation of high quality DNA (as specified above); ii) high reproducibility; iii) high reliability, iv) ease of handling; v) low handling effort; and vi) low costs.
Additionally, because in general the amount of the tissue sample or biopsy is very small, it is necessary that the methods for DNA preparation result in high yields of DNA.
Because of all these requirements, and given the prior art methods, archived samples, despite being a major resource in medical science, can only be minimally used for the efficient analysis of the DNA methylation. Thus, a major technical need exists to efficiently make archived samples (e.g., paraffin-embedded formalin-fixed tissues) available for the analysis of, for example, the DNA methylation patterns.
Thus far, applicants are aware of only one attempt to solve this problem. WO03/083107 teaches a method for isolation of genomic DNA from paraffin-embedded suitable for subsequent DNA methylation analysis by methylation specific PCR (MSP). In principle, the deparaffinated formalin-fixed sample is boiled in a citrate buffer pH 6.0, which recovers parts of the cytosines making them better accessible for subsequent treatment and analysis. However, this method is conflicting with regard to the aim to provide as long as possible DNA fragments. According to this method, DNA is brought into contact with a buffer of acidic pH. As is well known in the relevant art, such treatment reduces the integrity of DNA resulting in a random breakage of the DNA strand and therefore the length of the DNA fragments.